I have downloaded and installed the trial version of FrameMaker 12 to test the new publishing capability. My test document has five conditions, including one I would apply to paragraphs that anchor graphics frames.

When I hide all conditional text, either by moving all conditions to the Hide text box or by applying the expression:

not "Condition1" and not ( "Condition2" or "Condition3" or "Condition4" or "Condition5")

and then "Publish" to Microsoft HTML Help, the resulting help file still shows the paragraphs I want hidden. The same thing happens if I select WebHelp.

This sounds like you may have stumbled into a bug with the sts files (these are simply zip containers that hold all of the individual settings files). Can you narrow down what the difference in the settings are between the sts file where the conditions work and where they don't?